Carbocation scavenging during oligonucleotide synthesis
AssigneeIsis Pharmaceuticals, Inc.
InventorsVasulinga Ravikumar, Mark Andrade, Dennis Mulvey, Douglas L. Cole
Life of this patent
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Abstract
During the synthesis of oligonucleotides and phosphate linked oligomers, a carbocation scavenging agent is employed to increase the overall yield. The carbocation scavenging agent is used in conjunction with an acidic solution employed during the deprotection step.
Claims24
A process for the synthesis of oligonucleotides comprising the steps of:
- a) attaching a protected nucleoside to a solid support, said nucleoside protected at the 5'-O hydroxyl position with an acid labile protecting group that forms a carbocation upon cleavage with acid;
- b) removing said 5' protecting group with an acidic solution containing a carbocation scavenging agent to give the free 5' hydroxyl;
- c) washing said solid support to remove excess acid solution and scavenged carbocation;
- d) reacting in the presence of a catalyst said free 5' hydroxyl with a nucleotide containing an active phosphite;
- e) oxidizing the phosphite to a phosphate;
- f) capping remaining reactive sites with a solution containing an acid anhydride;
- g) repeating steps b through f at least once for subsequent couplings of additional nucleotides;
- and
- h) cleaving said oligonucleotide from said solid support.
A process for the synthesis of oligonucleotides comprising the steps of:
- a) providing a nucleoside that is protected at the 3' hydroxyl position with a base labile protecting group and further protected at the 5' hydroxyl position with an acid labile protecting group that forms a carbocation upon cleavage with acid;
- b) removing said 5' protecting group with an acidic solution, said solution containing a carbocation scavenging agent, to give the free 5' hydroxyl nucleoside;
- c) reacting in the presence of a catalyst said free 5' hydroxyl with a nucleotide containing an active phosphite;
- d) oxidizing the phosphite to a phosphate;
- e) capping remaining reactive sites with a solution containing an acid anhydride;
- f) repeating steps b through e at least once for subsequent couplings to additional nucleotides;
- and
- g) cleaving the 3' hydroxyl base labile protecting group with a basic solution.
A method for preparing an oligonucleotide, comprising protecting a 5' hydroxyl or 3' hydroxyl group of the ribose or deoxyribose portion of a 5' of 3' terminal nucleoside of said oligonucleotide, with an acid labile protecting group that releases a carbocation when treated with acid, and
- removing said carbocation by the addition of a carbocation scavenging agent.
Dependencies are inferred from the claim text.